rs716501

Variant names:

• chr4-122430770-G-A
• rs716501

Your query was ambiguous. Multiple possible variants found:

• chr4-122430770-G-A
• chr4-122430770-G-C
• chr4-122430770-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.29 in 151,946 control chromosomes in the GnomAD database, including 7,536 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.29 (7536 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.970
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44048 AN: 151828 Hom.: 7535 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.271

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.290 AC: 44050 AN: 151946 Hom.: 7536 Cov.: 32 AF XY: 0.297 AC XY: 22045 AN XY: 74254

African (AFR) AF: 0.116 AC: 4812 AN: 41500

American (AMR) AF: 0.396 AC: 6043 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 734 AN: 3464

East Asian (EAS) AF: 0.478 AC: 2468 AN: 5164

South Asian (SAS) AF: 0.263 AC: 1269 AN: 4820

European-Finnish (FIN) AF: 0.471 AC: 4959 AN: 10532

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22961 AN: 67890

Other (OTH) AF: 0.271 AC: 572 AN: 2110

Alfa AF: 0.316 Hom.: 5161

Bravo AF: 0.280

Asia WGS AF: 0.298 AC: 1031 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.79
DANN	Benign	0.74
PhyloP100		-0.97

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs716501; hg19: chr4-123351925;